Journal of Theoretical
and Applied Mechanics

56, 3, pp. 601-614, Warsaw 2018
DOI: 10.15632/jtam-pl.56.3.601

Coarse-graining models for molecular dynamics simulations of FCC metals

Pourya Delafrouz, Hossein Nejat Pishkenari
In this paper, four coarse-graining (CG) models are proposed to accelerate molecular dynamics
simulations of FCC metals. To this aim, at first, a proper map between beads of the
CG models and atoms of the all-atom (AA) system is assigned, afterwards mass of the beads
and the parameters of the CG models are determined in a manner that the CG models and
the original all-atom model have the same physical properties. To evaluate and compare
precision of these four CG models, different static and dynamic simulations are conducted.
The results show that these CG models are at least 4 times faster than the AA model, while
their errors are less than 1 percent.
Keywords: accelerated molecular dynamics, coarse-grain models, FCC metals, EAM potential

References


Berg B.A., 2005, Introduction to Markov chain Monte Carlo simulations and their statistical

analysis, Markov Chain Monte Carlo, Lecture Notes Series, 7, 1

Burbery N., Das R., Ferguson W., 2017, Dynamic behaviour of mixed dislocations in FCC

metals under multi-oriented loading with molecular dynamics simulations, Computational Materials

Science, 137, 39-54

Cascella M., Dal Peraro M., 2009, Challenges and perspectives in biomolecular simulations:

from the atomistic picture to multiscale modeling, CHIMIA International Journal for Chemistry, 63, 14-18

Chandramouli P.N., 2014, Continuum Mechanics, Yes Dee Publishing Pvt Ltd.

Chen Y., Zimmerman J., Krivtsov A., McDowell D.L., 2011, Assessment of atomistic

coarse-graining methods, International Journal of Engineering Science, 49, 1337-1349

Cranford S., Buehler M.J., 2010, Coarse-Graining Parameterization and Multiscale Simula-

tion of Hierarchical Systems. Part I: Theory and Model Formulation, DTIC Document

Hedrih K.R.S., Hedrih A.N., 2010, Eigen modes of the double DNA chain helix vibrations,

Journal of Theoretical and Applied Mechanics, 48, 219-231

Hoover W.G., 1985, Canonical dynamics: equilibrium phase-space distributions, Physical Review

A, 31, 1695

Jovanovic A.S., Filipovic N., 2006, Innovative modeling methods in damage assessment: application

of dissipative particle dynamics to simulation of damage and self-healing of polymer-coated

surfaces, Journal of Theoretical and Applied Mechanics, 44, 637-648

Karma A., Tourret D., 2016, Atomistic to continuum modeling of solidification microstructures,

Current Opinion in Solid State and Materials Science, 20, 25-36

Lao J., Tam M.N., Pinisetty D., Gupta N., 2013, Molecular dynamics simulation of FCC

metallic nanowires: a review, JOM, 65, 175-184

Leach A.R., 2001, Molecular Modelling: Principles and Applications, Pearson education

Marrink S.J., Risselada H.J., Yefimov S., Tieleman D.P., de Vries A.H., 2007, The

MARTINI force field: coarse grained model for biomolecular simulations, The Journal of Physical

Chemistry B, 111, 7812-7824

Muc A,, 2011,Modelling of carbon nanotubes behaviour with the use of a thin shell theory, Journal

of Theoretical and Applied Mechanics, 49, 531-540

Nos´e S., 1984, A unified formulation of the constant temperature molecular dynamics methods,

The Journal of Chemical Physics, 81, 511-519

Oren E., Yahel E., Makov G., 2016, Dislocation kinematics: a molecular dynamics study in

Cu, Modelling and Simulation in Materials Science and Engineering, 25, 025002

Ouldridge T.E., 2012, Coarse-Grained Modelling of DNA and DNA Self-Assembly, Springer

Paćko P., Uhl T., 2011, Multiscale approach to structure damage modelling, Journal of Theore-

tical and Applied Mechanics, 49, 243-264

Park H.S., Klein P.A., 2007, Surface Cauchy-Born analysis of surface stress effects on metallic

nanowires, Physical Review B, 75, 085408

Pishkenari H.N., 2015, Atomic interactions between metallic tips and surfaces in NC-AFM,

Journal of Physics D: Applied Physics, 48, 125301

Pishkenari H.N., Afsharmanesh B., Akbari E., 2015, Surface elasticity and size effect on the

vibrational behavior of silicon nanoresonators, Current Applied Physics, 15, 1389-1396

Pishkenari H.N., Afsharmanesh B., Tajaddodianfar F., 2016, Continuum models calibrated

with atomistic simulations for the transverse vibrations of silicon nanowires, International Journal

of Engineering Science, 100, 8-24

Pishkenari H.N., Meghdari A., 2010, Surface defects characterization with frequency and force

modulation atomic force microscopy using molecular dynamics simulations, Current Applied

Physics, 10, 583-591

Plimpton S., 1995, Fast parallel algorithms for short-range molecular dynamics, Journal of Com-

putational Pphysics, 117, 1-19

Poursina M., Anderson K.S., 2014, An improved fast multipole method for electrostatic potential

calculations in a class of coarse-grained molecular simulations, Journal of Computational

Physics, 270, 613-633

Samani M., Pourtakdoust S.H., 2014, Analysis of two-stage endo-atmospheric separation using

statistical methods, Journal of Theoretical and Applied Mechanics, 52, 1115-1124

Simmons G., Wang H., 1971, Single Crystal Elastic Constants and Calculated Aggregate Proper-

ties, 2nd ed., Cambridge, Mass., M.I.T. Press

Tadmor E., Legoll F., Kim W., Dupuy L., Miller R., 2013, Finite-temperature quasi-

-continuum, Applied Mechanics Reviews, 65, 010803, 2013

Yang S., Qu J., 2014, An investigation of the tensile deformation and failure of an epoxy/Cu interface

using coarse-grained molecular dynamics simulations, Modelling and Simulation in Materials

Science and Engineering, 22, 065011

Yang Q., To A.C., 2015, Multiresolution molecular mechanics: A unified and consistent framework

for general finite element shape functions, Computer Methods in Applied Mechanics and

Engineering, 283, 384-418

Zhou X., Johnson R., Wadley H., 2004, Misfit-energy-increasing dislocations in vapor-

-deposited CoFe/NiFe multilayers, Physical Review B, 69, 144113